title: Surveillance on A/H5N1 virus in domestic poultry and wild birds in Egypt.
abstract: BACKGROUND
  The endemic H5N1 high pathogenicity avian influenza virus (A/H5N1) in poultry in Egypt continues to cause heavy losses in poultry and poses a significant threat to human health.
  
  
  METHODS
  Here we describe results of A/H5N1 surveillance in domestic poultry in 2009 and wild birds in 2009-2010. Tracheal and cloacal swabs were collected from domestic poultry from 22024 commercial farms, 1435 backyards and 944 live bird markets (LBMs) as well as from 1297 wild birds representing 28 different types of migratory birds. Viral RNA was extracted from a mix of tracheal and cloacal swabs media. Matrix gene of avian influenza type A virus was detected using specific real-time reverse-transcription polymerase chain reaction (RT-qPCR) and positive samples were tested by RT-qPCR for simultaneous detection of the H5 and N1 genes.
  
  
  RESULTS
  In this surveillance, A/H5N1 was detected from 0.1% (n = 23/) of examined commercial poultry farms, 10.5% (n = 151) of backyard birds and 11.4% (n = 108) of LBMs but no wild bird tested positive for A/H5N1. The virus was detected from domestic poultry year-round with higher incidence in the warmer months of summer and spring particularly in backyard birds. Outbreaks were recorded mostly in Lower Egypt where 95.7% (n = 22), 68.9% (n = 104) and 52.8% (n = 57) of positive commercial farms, backyards and LBMs were detected, respectively. Higher prevalence (56%, n = 85) was reported in backyards that had mixed chickens and waterfowl together in the same vicinity and LBMs that had waterfowl (76%, n = 82).
  
  
  CONCLUSIONS
  Our findings indicated broad circulation of the endemic A/H5N1 among poultry in 2009 in Egypt. In addition, the epidemiology of A/H5N1 has changed over time with outbreaks occurring in the warmer months of the year. Backyard waterfowl may play a role as a reservoir and/or source of A/H5N1 particularly in LBMs. The virus has been established in poultry in the Nile Delta where major metropolitan areas, dense human population and poultry stocks are concentrated. Continuous surveillance, tracing the source of live birds in the markets and integration of multifaceted strategies and global collaboration are needed to control the spread of the virus in Egypt.
authors.affiliation: National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, PO Box 246, Giza 12618, Egypt.
authors.forename: Elham F
authors.initials: EF
authors.lastname: El-Zoghby
authors.forename: Mona M
authors.initials: MM
authors.lastname: Aly
authors.forename: Soad A
authors.initials: SA
authors.lastname: Nasef
authors.forename: Mohamed K
authors.initials: MK
authors.lastname: Hassan
authors.forename: Abdel-Satar
authors.initials: AS
authors.lastname: Arafa
authors.forename: Abdullah A
authors.initials: AA
authors.lastname: Selim
authors.forename: Shereen G
authors.initials: SG
authors.lastname: Kholousy
authors.forename: Walid H
authors.initials: WH
authors.lastname: Kilany
authors.forename: Marwa
authors.initials: M
authors.lastname: Safwat
authors.forename: E M
authors.initials: EM
authors.lastname: Abdelwhab
authors.forename: Hafez M
authors.initials: HM
authors.lastname: Hafez
mesh_terms: D000818:Animals; D001717:Birds; D002988:Cloaca / Q000821:virology; D004196:Disease Outbreaks; D004534:Egypt / Q000453:epidemiology; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics / Q000302:isolation & purification*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology*; D009439:Neuraminidase / Q000235:genetics; D011200:Poultry; D015995:Prevalence; D060888:Real-Time Polymerase Chain Reaction; D012621:Seasons; D014132:Trachea / Q000821:virology; D014763:Viral Matrix Proteins / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; C488936:M1 protein, Influenza A virus; D014763:Viral Matrix Proteins; D014764:Viral Proteins; C109963:hemagglutinin, avian influenza A virus; C487630:NA protein, influenza A virus; D009439:Neuraminidase